Although river ecosystems constitute a small fraction of Earth’s total area, they are critical modulators of microbially and virally orchestrated global biogeochemical cycles. However, most studies either use data that is not spatially resolved or is collected at timepoints that do not reflect the short life cycles of microorganisms. To address this gap, we assessed how viral and microbial communities change over a 48-hour period by sampling surface water and pore water compartments of the wastewater-impacted River Erpe in Germany. We sampled every 3 hours resulting in 32 samples for which we obtained metagenomes along with geochemical and metabolite measurements. From our metagenomes, we identified 6,500 viral and 1,033 microbial metagenome assembled genomes (MAGs) and found distinct community membership and abundance associated with each river compartment (e.g., Competibacteraceae in surfacewater and Sulfurimonadaceae in pore water). We show that 17% of our viral MAGs clustered to viruses from other ecosystems like wastewater treatment plants and rivers. Our results also indicated that 70% of the viral community was persistent in surface waters, whereas only 13% were persistent in the pore waters taken from the hyporheic zone. Finally, we predicted linkages between 73 viral genomes and 38 microbial genomes. These putatively linked hosts included members of the Competibacteraceae, which we suggest are potential contributors to river carbon and nitrogen cycling via denitrification and nitrogen fixation. Together, these findings demonstrate that members of the surface water microbiome from this urban river are stable over multiple diurnal cycles. These temporal insights raise important considerations for ecosystem models attempting to constrain dynamics of river biogeochemical cycles.
Rodríguez-Ramos, Josué, et al. "Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream." Frontiers in Microbiomes, vol. 2, Aug. 2023. https://doi.org/10.3389/frmbi.2023.1199766
Rodríguez-Ramos, Josué, Oliverio, Angela, Borton, Mikayla A., Danczak, Robert, Mueller, Birgit M., Schulz, Hanna, Ellenbogen, Jared, Flynn, Rory M., Daly, Rebecca A., Schopflin, LeAundra, Shaffer, Michael, Goldman, Amy, Lewandowski, Joerg, Stegen, James C., & Wrighton, Kelly C. (2023). Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream. Frontiers in Microbiomes, 2. https://doi.org/10.3389/frmbi.2023.1199766
Rodríguez-Ramos, Josué, Oliverio, Angela, Borton, Mikayla A., et al., "Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream," Frontiers in Microbiomes 2 (2023), https://doi.org/10.3389/frmbi.2023.1199766
@article{osti_1994452,
author = {Rodríguez-Ramos, Josué and Oliverio, Angela and Borton, Mikayla A. and Danczak, Robert and Mueller, Birgit M. and Schulz, Hanna and Ellenbogen, Jared and Flynn, Rory M. and Daly, Rebecca A. and Schopflin, LeAundra and others},
title = {Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream},
annote = {Although river ecosystems constitute a small fraction of Earth’s total area, they are critical modulators of microbially and virally orchestrated global biogeochemical cycles. However, most studies either use data that is not spatially resolved or is collected at timepoints that do not reflect the short life cycles of microorganisms. To address this gap, we assessed how viral and microbial communities change over a 48-hour period by sampling surface water and pore water compartments of the wastewater-impacted River Erpe in Germany. We sampled every 3 hours resulting in 32 samples for which we obtained metagenomes along with geochemical and metabolite measurements. From our metagenomes, we identified 6,500 viral and 1,033 microbial metagenome assembled genomes (MAGs) and found distinct community membership and abundance associated with each river compartment (e.g., Competibacteraceae in surfacewater and Sulfurimonadaceae in pore water). We show that 17% of our viral MAGs clustered to viruses from other ecosystems like wastewater treatment plants and rivers. Our results also indicated that 70% of the viral community was persistent in surface waters, whereas only 13% were persistent in the pore waters taken from the hyporheic zone. Finally, we predicted linkages between 73 viral genomes and 38 microbial genomes. These putatively linked hosts included members of the Competibacteraceae, which we suggest are potential contributors to river carbon and nitrogen cycling via denitrification and nitrogen fixation. Together, these findings demonstrate that members of the surface water microbiome from this urban river are stable over multiple diurnal cycles. These temporal insights raise important considerations for ecosystem models attempting to constrain dynamics of river biogeochemical cycles.},
doi = {10.3389/frmbi.2023.1199766},
url = {https://www.osti.gov/biblio/1994452},
journal = {Frontiers in Microbiomes},
issn = {ISSN 2813-4338},
volume = {2},
place = {United States},
publisher = {Frontiers Media SA},
year = {2023},
month = {08}}
Wells, Jacqueline R.; Goldman, Amy E.; Chu, Rosalie K.
Environmental System Science Data Infrastructure for a Virtual Ecosystem; Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS)https://doi.org/10.15485/1577260